Back in the '70's & '80's, considering the quality of the parts for -3's & -4's, it was not uncommon to have the problem you speak of.
Remember, this is back in the time when ALL holes/specs were the responsibility of the builder. This means if the motor mount (if square? Maybe not - did you check during the build) was mounted square to the airframe - it could still mean that the GL sleeves were not. The GL sleeves could have been slightly misaligned during the welding sequence.
It turned out on a lot of the builds I watched (and participated in) in the Bakersfield, CA area had sockets that had a slight misalignment; and, required the gearlegs to be moved up/down so the fuse would not have the "leans". Typically one leg (the left as I remember) would "stick" up about and 1/8" above the top of the GL sleeve. After a level position (side-to-side) of the fuselage was achieved - only then were the legs drilled to the sockets.
Don't know about early -6's or others - but any of the early builds that relied entirely on the builder's accuracy for layout to specs, could easily be called into question.
This may not be what has happened in your case - but there are probably no GL parts on these airplanes that are interchangeable without compromise.
HFS
RV-4 S/N 1136 (1985)